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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ), 'gf_id' => 'HOM05D001213', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001213' ), 'data_identifier' => 'HOM05D001213', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001213', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '516', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p04230' => 'bna', 'A04p06500' => 'bna', 'A09p46070' => 'bna', 'Aa31LG10G8220' => 'aar', 'Aa31LG2G16690' => 'aar', 'Aa31LG2G16710' => 'aar', 'Aa31LG2G16720' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1135' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1136' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.577' => 'aag', 'Actinidia00414' => 'ach', 'Actinidia01076' => 'ach', 'Actinidia17476' => 'ach', 'Actinidia38083' => 'ach', 'Actinidia38084' => 'ach', 'Actinidia38085' => 'ach', 'Ah.01g018200' => 'amhyb', 'Ah.05g167270' => 'amhyb', 'Ah.11g043060' => 'amhyb', 'AL5G33820' => 'aly', 'AL7G17100' => 'aly', 'Aqoxy5G01148' => 'aox', 'Aqoxy5G01149' => 'aox', 'Aqoxy6G02885' => 'aox', 'Aqoxy6G02886' => 'aox', 'arahy.Tifrunner.gnm1.ann1.BMP346' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LJ1TN7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZE0Q8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UH3WW7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUTQ0L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLB5X0' => 'arhy', 'AT3G53010' => 'ath', 'AT4G34215' => 'ath', 'ATR0789G007' => 'atr', 'Atru.chr13.756' => 'acertr', 'Atru.chr13.759' => 'acertr', 'Atru.chr13.760' => 'acertr', 'Atru.chr13.761_Atru.chr13.763' => 'acertr', 'Atru.chr5.2584' => 'acertr', 'Atru.chr5.2585' => 'acertr', 'AUR62010287' => 'cqu', 'AUR62010288' => 'cqu', 'AUR62039102' => 'cqu', 'AUR62041685' => 'cqu', 'AUR62041686' => 'cqu', 'AUR62043034' => 'cqu', 'AUR62043035' => 'cqu', 'BcaB01g00317' => 'bca', 'BcaB02g08544' => 'bca', 'BcaC02g09197' => 'bca', 'BcaC07g39664' => 'bca', 'BcaNung03803' => 'bca', 'BcaNung03804' => 'bca', 'BolC1t00445H' => 'bol', 'BolC4t25567H' => 'bol', 'BolC8t50441H' => 'bol', 'BraA01t00412Z' => 'bra', 'BraA04t16353Z' => 'bra', 'BraA09t40071Z' => 'bra', 'C01p04610' => 'bna', 'C04p39950' => 'bna', 'C08p28320' => 'bna', 'CAN.G101.19' => 'can', 'CAN.G1038.2' => 'can', 'CAN.G107.46' => 'can', 'CAN.G1248.8' => 'can', 'CAN.G1621.2' => 'can', 'CAN.G1621.3' => 'can', 'CAN.G170.112' => 'can', 'CAN.G170.113' => 'can', 'CAN.G170.118' => 'can', 'CAN.G1812.7' => 'can', 'CAN.G65.167' => 'can', 'CANSAT25G0734' => 'cansat', 'CANSAT25G1249' => 'cansat', 'CANSAT25G1949' => 'cansat', 'CANSAT25G2741' => 'cansat', 'CANSAT25G2765' => 'cansat', 'CANSAT25G3655' => 'cansat', 'CARHR162900' => 'chi', 'CARHR242580' => 'chi', 'Carub.0005s1951' => 'cru', 'Carub.0007s0617' => 'cru', 'Ca_11081_v3' => 'car', 'Ca_13254_v3' => 'car', 'Ca_15930_v3' => 'car', 'Cc01_g11030' => 'ccan', 'Cc02_g19210' => 'ccan', 'Cc10_g04910' => 'ccan', 'Cc10_g04930' => 'ccan', 'CDE02G1338' => 'cde', 'CDE02G3453' => 'cde', 'CDE04G2876' => 'cde', 'Cfa002323' => 'cfa', 'Cfa004572' => 'cfa', 'Cfa009952' => 'cfa', 'Cfa009953' => 'cfa', 'Cfa009954' => 'cfa', 'Cfa009955' => 'cfa', 'Cfa018059' => 'cfa', 'Ciclev10001964m.g' => 'ccl', 'Ciclev10029126m.g' => 'ccl', 'CiPaw.03G257100' => 'cil', 'CiPaw.04G181700' => 'cil', 'CiPaw.05G011000' => 'cil', 'CiPaw.16G036800' => 'cil', 'CiPaw.16G036900' => 'cil', 'CiPaw.16G038900' => 'cil', 'CiPaw.16G039000' => 'cil', 'CiPaw.16G039300' => 'cil', 'CiPaw.16G039400' => 'cil', 'CiPaw.16G039500' => 'cil', 'CiPaw.16G039700' => 'cil', 'CiPaw.16G054100' => 'cil', 'CiPaw.16G067900' => 'cil', 'CiPaw.16G068000' => 'cil', 'CiPaw.16G070600' => 'cil', 'CiPaw.16G070700' => 'cil', 'CiPaw.16G070800' => 'cil', 'ClCG00G006520' => 'cla', 'ClCG02G006300' => 'cla', 'ClCG05G020250' => 'cla', 'ClCG07G001770' => 'cla', 'ClCG08G006890' => 'cla', 'ClCG08G016180' => 'cla', 'ClCG08G016190' => 'cla', 'ClCG08G016200' => 'cla', 'ClCG10G013020' => 'cla', 'COL.COLO4_10107' => 'col', 'COL.COLO4_10108' => 'col', 'COL.COLO4_32601' => 'col', 'Cpa.g.sc106.87' => 'cpa', 'Cpa.g.sc21.147' => 'cpa', 'Cre07.g344000' => 'cre', 'Cre17.g744297' => 'cre', 'CsaV3_2G026420' => 'csa', 'CsaV3_2G026430' => 'csa', 'CsaV3_2G026440' => 'csa', 'CsaV3_4G034730' => 'csa', 'CsaV3_6G005350' => 'csa', 'CsaV3_6G005360' => 'csa', 'CsaV3_6G013380' => 'csa', 'CsaV3_7G008110' => 'csa', 'CsaV3_UNG024150' => 'csa', 'CsaV3_UNG028150' => 'csa', 'CSS0006718' => 'camsi', 'CSS0009601' => 'camsi', 'CSS0025622' => 'camsi', 'CSS0040848' => 'camsi', 'CSS0042799' => 'camsi', 'DCAR_008823' => 'dca', 'DCAR_021993' => 'dca', 'Dinv35920' => 'din', 'Dinv39268' => 'din', 'Dinv42188' => 'din', 'Duzib052G0447' => 'dzi', 'Duzib093G1248' => 'dzi', 'Duzib093G2257' => 'dzi', 'Duzib116G0748' => 'dzi', 'Duzib248G0154' => 'dzi', 'ECA232G1149' => 'eca', 'ECA232G1515' => 'eca', 'ECA232G3173' => 'eca', 'ECA234G0447' => 'eca', 'ECA247G1314' => 'eca', 'ECA247G3295' => 'eca', 'EL10Ac9g22287' => 'bvu', 'EL10As7g23789' => 'bvu', 'Eucgr.F00001' => 'egr', 'Eucgr.F00179' => 'egr', 'Eucgr.F02295' => 'egr', 'Eucgr.F02296' => 'egr', 'Eucgr.F02298' => 'egr', 'Eucgr.H03215' => 'egr', 'Eucgr.H03219' => 'egr', 'Eucgr.L02594' => 'egr', 'FAN15G0427' => 'fan', 'FAN15G0606' => 'fan', 'FAN15G1995' => 'fan', 'FAN20G1084' => 'fan', 'FAN20G2322' => 'fan', 'FAN24G0806' => 'fan', 'FAN24G1472' => 'fan', 'FAN27G0579' => 'fan', 'FvH4_2g05290' => 'fve', 'FvH4_2g33790' => 'fve', 'FvH4_2g33800' => 'fve', 'Glyma.04G042200' => 'gma', 'Glyma.06G043100' => 'gma', 'Glyma.10G261500' => 'gma', 'Glyma.14G086400' => 'gma', 'Glyma.17G238000' => 'gma', 'Glyma.20G129300' => 'gma', 'Gohir.A01G007900' => 'ghi', 'Gohir.A05G206100' => 'ghi', 'Gohir.A05G262300' => 'ghi', 'Gohir.A06G021700' => 'ghi', 'Gohir.A06G021800' => 'ghi', 'Gohir.D01G008000' => 'ghi', 'Gohir.D05G209400' => 'ghi', 'Gohir.D05G264500' => 'ghi', 'Gohir.D06G019200' => 'ghi', 'Gohir.D06G019300' => 'ghi', 'Gorai.002G009200' => 'gra', 'Gorai.009G215800' => 'gra', 'Gorai.009G276300' => 'gra', 'Gorai.010G023300' => 'gra', 'Gorai.010G023400' => 'gra', 'GSVIVG01003163001' => 'vvi', 'GSVIVG01009426001' => 'vvi', 'GSVIVG01009427001' => 'vvi', 'HanXRQChr02g0038031' => 'han', 'HanXRQChr09g0267361' => 'han', 'HanXRQChr10g0301611' => 'han', 'HanXRQChr10g0309631' => 'han', 'HanXRQChr11g0345621' => 'han', 'HanXRQChr11g0345631' => 'han', 'HanXRQChr11g0345651' => 'han', 'HanXRQChr11g0345721' => 'han', 'HanXRQChr11g0345731' => 'han', 'HanXRQChr11g0345751' => 'han', 'HanXRQChr11g0345761' => 'han', 'HanXRQChr16g0514861' => 'han', 'Haze_10164' => 'cav', 'Haze_18050' => 'cav', 'Haze_18051' => 'cav', 'Haze_18052' => 'cav', 'Haze_24528' => 'cav', 'Hma1.2p1_0240F.1_g100280' => 'hma', 'Hma1.2p1_0634F.1_g193000' => 'hma', 'HPP92_014602' => 'vpl', 'HPP92_014606' => 'vpl', 'HPP92_014607' => 'vpl', 'HPP92_017267' => 'vpl', 'HPP92_017278' => 'vpl', 'HPP92_028772' => 'vpl', 'Hund00146' => 'sun', 'Hund24094' => 'sun', 'Lalb_Chr02g0145331' => 'lal', 'Lalb_Chr11g0062731' => 'lal', 'Lalb_Chr22g0354861' => 'lal', 'Lalb_Chr23g0267311' => 'lal', 'Lj1C613T0' => 'lonja', 'Lj1g0012355' => 'lja', 'Lj4A765T42' => 'lonja', 'Lj4C65T1' => 'lonja', 'Lj5A213T90' => 'lonja', 'Lj5g0025804' => 'lja', 'Lj5g0028238' => 'lja', 'Lsat_1_v5_gn_1_22580' => 'lsa', 'Lsat_1_v5_gn_1_22980' => 'lsa', 'Lsat_1_v5_gn_4_128580' => 'lsa', 'Lsat_1_v5_gn_4_128600' => 'lsa', 'Lsat_1_v5_gn_4_128621' => 'lsa', 'Lsat_1_v5_gn_4_128741' => 'lsa', 'Lsat_1_v5_gn_5_114761' => 'lsa', 'Manes.05G177700' => 'mes', 'Manes.05G177800' => 'mes', 'Manes.10G073700' => 'mes', 'Manes.18G041900' => 'mes', 'Mapoly0001s0114' => 'mpo', 'MBI16_g40014_MAGBIO' => 'mbi', 'MCO11G033' => 'mco', 'MD08G1092200' => 'mdo', 'MD15G1076700' => 'mdo', 'MD15G1076800' => 'mdo', 'Medtr1g018750' => 'mtr', 'Medtr1g107475' => 'mtr', 'Medtr3g102390' => 'mtr', 'Medtr4g031010' => 'mtr', 'MELO3C000409.2' => 'cme', 'MELO3C000816.2' => 'cme', 'MELO3C008368.2' => 'cme', 'MELO3C010834.2' => 'cme', 'MELO3C016788.2' => 'cme', 'MELO3C018495.2' => 'cme', 'MELO3C030338.2' => 'cme', 'MELO3C030490.2' => 'cme', 'MELO3C030746.2' => 'cme', 'Migut.C00525' => 'egut', 'Migut.C00526' => 'egut', 'Migut.C00527' => 'egut', 'Migut.C00528' => 'egut', 'Migut.N01169' => 'egut', 'Migut.N01170' => 'egut', 'MSTRG.1054' => 'ama', 'MSTRG.24383' => 'ama', 'MSTRG.5344' => 'ama', 'Nitab4.5_0000232g0250' => 'nta', 'Nitab4.5_0000412g0040' => 'nta', 'Nitab4.5_0000421g0030' => 'nta', 'Nitab4.5_0000634g0180' => 'nta', 'Nitab4.5_0001186g0090' => 'nta', 'Nitab4.5_0001211g0290' => 'nta', 'Nitab4.5_0001676g0010' => 'nta', 'Nitab4.5_0001984g0060' => 'nta', 'Nitab4.5_0002084g0050' => 'nta', 'Nitab4.5_0002098g0030' => 'nta', 'Nitab4.5_0002179g0050' => 'nta', 'Nitab4.5_0003597g0020' => 'nta', 'Nitab4.5_0004339g0010' => 'nta', 'Nitab4.5_0004339g0020' => 'nta', 'Nitab4.5_0005060g0010' => 'nta', 'Nitab4.5_0005198g0020' => 'nta', 'Nitab4.5_0005198g0050' => 'nta', 'Nitab4.5_0005777g0020' => 'nta', 'Nitab4.5_0005777g0040' => 'nta', 'Nitab4.5_0005794g0010' => 'nta', 'Nitab4.5_0005900g0100' => 'nta', 'Nitab4.5_0006486g0010' => 'nta', 'Nitab4.5_0007559g0010' => 'nta', 'Nitab4.5_0008244g0020' => 'nta', 'Nitab4.5_0008600g0020' => 'nta', 'Nitab4.5_0010118g0050' => 'nta', 'Nitab4.5_0010210g0020' => 'nta', 'Nn1g04709' => 'nnu', 'Nn5g30411' => 'nnu', 'Nn5g30412' => 'nnu', 'Oeu004560.1' => 'oeu', 'Oeu013748.1' => 'oeu', 'Oeu016593.1' => 'oeu', 'Oeu016595.1' => 'oeu', 'Oeu016601.1' => 'oeu', 'Oeu020223.1' => 'oeu', 'Oeu020224.1' => 'oeu', 'Oeu024272.1' => 'oeu', 'Oeu037607.1' => 'oeu', 'Oeu037608.1' => 'oeu', 'Oeu042613.1' => 'oeu', 'Oeu042614.1' => 'oeu', 'Oeu042618.1' => 'oeu', 'Oeu042621.1' => 'oeu', 'Oeu042622.1' => 'oeu', 'Oeu044288.1' => 'oeu', 'Oeu044854.1' => 'oeu', 'Oeu044855.1' => 'oeu', 'Oeu045715.1' => 'oeu', 'Oeu056380.1' => 'oeu', 'Oeu056382.1' => 'oeu', 'Oeu056387.1' => 'oeu', 'Os03g0857500' => 'osa', 'Os03g0857600' => 'osa', 'Os04g0110400' => 'osa', 'Os04g0276600' => 'osa', 'Peaxi162Scf00041g01735' => 'pax', 'Peaxi162Scf00071g01135' => 'pax', 'Peaxi162Scf00160g00038' => 'pax', 'Peaxi162Scf00160g01328' => 'pax', 'Peaxi162Scf00160g01336' => 'pax', 'Peaxi162Scf00173g01213' => 'pax', 'Peaxi162Scf00229g01514' => 'pax', 'Peaxi162Scf00229g01515' => 'pax', 'Peaxi162Scf00405g00148' => 'pax', 'Peaxi162Scf00405g01326' => 'pax', 'Peaxi162Scf00413g00514' => 'pax', 'Peaxi162Scf00428g00212' => 'pax', 'Peaxi162Scf00428g00623' => 'pax', 'Peaxi162Scf00679g00004' => 'pax', 'Peaxi162Scf00679g00014' => 'pax', 'Peaxi162Scf00695g00049' => 'pax', 'Peaxi162Scf01087g00122' => 'pax', 'PGR004G0082' => 'pgr', 'PGR031G0134' => 'pgr', 'PGR031G1884' => 'pgr', 'PGR031G2192' => 'pgr', 'PGR042G2177' => 'pgr', 'PGR042G2754' => 'pgr', 'PGR102G2069' => 'pgr', 'PGR102G2688' => 'pgr', 'PGSC0003DMG400003314' => 'stu', 'PGSC0003DMG400003315' => 'stu', 'PGSC0003DMG400006404' => 'stu', 'PGSC0003DMG400006876' => 'stu', 'PGSC0003DMG400008003' => 'stu', 'PGSC0003DMG400008544' => 'stu', 'PGSC0003DMG400008606' => 'stu', 'PGSC0003DMG400015432' => 'stu', 'PGSC0003DMG400018238' => 'stu', 'PGSC0003DMG400026915' => 'stu', 'PGSC0003DMG400038766' => 'stu', 'PGSC0003DMG400043390' => 'stu', 'PGSC0003DMG401006875' => 'stu', 'PGSC0003DMG402006875' => 'stu', 'Phvul.001G025101' => 'pvu', 'Phvul.007G040500' => 'pvu', 'Phvul.009G067900' => 'pvu', 'Potri.001G300800' => 'ptr', 'Potri.009G096400' => 'ptr', 'Potri.009G096500' => 'ptr', 'Potri.014G022600' => 'ptr', 'Potri.014G022700' => 'ptr', 'Pp3c2_27970' => 'ppa', 'PRCOL_00002978' => 'pco', 'Prupe.1G430100' => 'ppe', 'Prupe.1G430200' => 'ppe', 'Prupe.8G134400' => 'ppe', 'Psat5g041440' => 'psa', 'Psat6g014080' => 'psa', 'Psat6g014120' => 'psa', 'Psat7g206560' => 'psa', 'PSO170G0816' => 'pso', 'PSO210G5431' => 'pso', 'PSO541G1620' => 'pso', 'PSO541G1799' => 'pso', 'PSO541G2453' => 'pso', 'PSO675G3651' => 'pso', 'PSO675G5695' => 'pso', 'PSO675G9348' => 'pso', 'QL02p003841' => 'qlo', 'QL02p003987' => 'qlo', 'QL11p033938' => 'qlo', 'QL12p042657' => 'qlo', 'RcHm_v2.0_Chr6g0255411' => 'rch', 'RcHm_v2.0_Chr6g0255421' => 'rch', 'RcHm_v2.0_Chr6g0308761' => 'rch', 'Rhsim05G0016100' => 'rsi', 'Rhsim07G0223900' => 'rsi', 'Rhsim07G0224100' => 'rsi', 'Rhsim07G0224500' => 'rsi', 'Rhsim07G0224600' => 'rsi', 'Rhsim07G0224700' => 'rsi', 'Rhsim07G0224800' => 'rsi', 'Rhsim07G0224900' => 'rsi', 'Rhsim07G0225000' => 'rsi', 'Rhsim11G0160500' => 'rsi', 'RhsimUnG0098300' => 'rsi', 'Sabra09G0074100' => 'sbr', 'Sabra14G0015000' => 'sbr', 'Sabra14G0015100' => 'sbr', 'Sabra14G0015200' => 'sbr', 'Sabra14G0015300' => 'sbr', 'Sabra14G0015400' => 'sbr', 'Sabra14G0015500' => 'sbr', 'Sabra14G0015600' => 'sbr', 'Sabra16G0188900' => 'sbr', 'SalBow1G0502' => 'sbo', 'SalBow1G4504' => 'sbo', 'SalBow1G6318' => 'sbo', 'SalBow1G7374' => 'sbo', 'SalBow3G2118' => 'sbo', 'SalBow3G2712' => 'sbo', 'SalBow3G2894' => 'sbo', 'SalBow7G1376' => 'sbo', 'SalBow7G2992' => 'sbo', 'Sc08g0001430' => 'sci', 'Sc15g0003460' => 'sci', 'Sed0012451' => 'sed', 'Sed0017298' => 'sed', 'Sed0019510' => 'sed', 'Sed0020848' => 'sed', 'Sed0021839' => 'sed', 'Sed0023344' => 'sed', 'SEGI_06730' => 'sgi', 'SEGI_16633' => 'sgi', 'SGA_v2.0_scaffold13G06607' => 'sas', 'SGA_v2.0_scaffold214G42254' => 'sas', 'SGA_v2.0_scaffold33G13444' => 'sas', 'SGA_v2.0_scaffold49G18095' => 'sas', 'SHI55155' => 'shi', 'SMO268G0002' => 'smo', 'Solyc01g087010.3' => 'sly', 'Solyc01g102330.3' => 'sly', 'Solyc04g074110.4' => 'sly', 'Solyc04g078430.3' => 'sly', 'Solyc04g078440.4' => 'sly', 'Solyc04g078530.3' => 'sly', 'Solyc06g073240.3' => 'sly', 'Solyc07g021505.1' => 'sly', 'Solyc07g021510.3' => 'sly', 'Solyc09g008540.1' => 'sly', 'Solyc12g057020.2' => 'sly', 'Solyc12g088640.2' => 'sly', 'Sopen01g034020' => 'spe', 'Sopen01g034100' => 'spe', 'Sopen01g044780' => 'spe', 'Sopen04g028620' => 'spe', 'Sopen04g029290' => 'spe', 'Sopen04g032040' => 'spe', 'Sopen04g032130' => 'spe', 'Sopen06g029600' => 'spe', 'Sopen09g003370' => 'spe', 'Sopen12g029680' => 'spe', 'Sopen12g030540' => 'spe', 'Sp5g09310' => 'spa', 'Sp7g31980' => 'spa', 'TAR628G0022' => 'tar', 'TAR628G0642' => 'tar', 'TAR628G0840' => 'tar', 'THA.LOC104807834' => 'tha', 'THA.LOC104825760' => 'tha', 'Thecc.02G107200' => 'tca', 'Thecc.08G000200' => 'tca', 'Thecc.08G000300' => 'tca', 'Thhalv10010602m.g' => 'esa', 'Thhalv10026018m.g' => 'esa', 'TPR.G20564' => 'tpr', 'TPR.G30566' => 'tpr', 'TWI56G1048' => 'twi', 'TWI56G1478' => 'twi', 'TWI79G0914' => 'twi', 'unitig_8.g5034' => 'ugi', 'vmacro02008' => 'vma', 'vmacro04565' => 'vma', 'vmacro04566' => 'vma', 'vmacro04567' => 'vma', 'vmacro04568' => 'vma', 'vmacro04569' => 'vma', 'vmacro04571' => 'vma', 'VMungo0647G1460' => 'vmu', 'VMungo0720G1046' => 'vmu', 'VMungo1309G1062' => 'vmu', 'Zm00001eb065000' => 'zma', 'Zm00001eb086990' => 'zma', 'Zm00001eb210460' => 'zma', 'Zm00001eb306610' => 'zma', 'Zm00001eb418480' => 'zma' ) $gf_id = 'HOM05D001213' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001213' ) $data_identifier = 'HOM05D001213' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 2, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 6, 'cqu' => (int) 7, 'bca' => (int) 6, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 11, 'cansat' => (int) 6, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 7, 'ccl' => (int) 2, 'cil' => (int) 17, 'cla' => (int) 9, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 10, 'camsi' => (int) 5, 'dca' => (int) 2, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 4, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 9, 'egut' => (int) 6, 'ama' => (int) 3, 'nta' => (int) 27, 'nnu' => (int) 3, 'oeu' => (int) 22, 'osa' => (int) 4, 'pax' => (int) 17, 'pgr' => (int) 8, 'stu' => (int) 14, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 1, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 11, 'sbr' => (int) 9, 'sbo' => (int) 9, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 2, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 12, 'spe' => (int) 11, 'spa' => (int) 2, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 2, 'twi' => (int) 3, 'ugi' => (int) 1, 'vma' => (int) 7, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418480' $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